Independencies Induced from a Graphical Markov Model After Marginalization and Conditioning: The R Package ggm

We describe some functions in the R package ggm to derive from a given Markov model, represented by a directed acyclic graph, different types of graphs induced after marginalizing over and conditioning on some of the variables. The package has a few basic functions that find the essential graph, the induced concentration and covariance graphs, and several types of chain graphs implied by the directed acyclic graph (DAG) after grouping and reordering the variables. These functions can be useful to explore the impact of latent variables or of selection effects on a chosen data generating model.

A gauge approach to the "pseudogap" phenomenology of the spectral weight in high Tc cuprates

We assume the t-t'-J model to describe the CuO_2 planes of hole-doped cuprates and we adapt the spin-charge gauge approach, previously developed for the t-J model, to describe the holes in terms of a spinless fermion carrying the charge (holon) and a neutral boson carrying spin 1/2 (spinon), coupled by a slave-particle gauge field. In this framework we consider the effects of a finite density of incoherent holon pairs in the normal state. Below a crossover temperature, identified as the experimental "upper pseudogap", the scattering of the "quanta" of the phase of the holon-pair field against holons reproduces the phenomenology of Fermi arcs coexisting with gap in the antinodal region. We thus obtain a microscopic derivation of the main features of the hole spectra due to pseudogap. This result is obtained through a holon Green function which follows naturally from the formalism and analytically interpolates between a Fermi liquid-like and a d-wave superconductor behavior as the coherence length of the holon pair order parameter increases. By inserting the gauge coupling with the spinon we construct explicitly the hole Green function and calculate its spectral weight and the corresponding density of states. So we prove that the formation of holon pairs induces a depletion of states on the hole Fermi surface. We compare our results with ARPES and tunneling experimental data. In our approach the hole preserves a finite Fermi surface until the superconducting transition, where it reduces to four nodes. Therefore we propose that the gap seen in the normal phase of cuprates is due to the thermal broadening of the SC-like peaks masking the Fermi-liquid peak. The Fermi arcs then correspond to the region of the Fermi surface where the Fermi-liquid peak is unmasked.Comment: 10 figures, comments and references added, 2 figures change

The statistical physics of active matter: from self-catalytic colloids to living cells

These lecture notes are designed to provide a brief introduction into the phenomenology of active matter and to present some of the analytical tools used to rationalize the emergent behavior of active systems. Such systems are made of interacting agents able to extract energy stored in the environment to produce sustained directed motion. The local conversion of energy into mechanical work drives the system far from equilibrium, yielding new dynamics and phases. The emerging phenomena can be classified depending on the symmetry of the active particles and on the type of microscopic interactions. We focus here on steric and aligning interactions, as well as interactions driven by shape changes. The models that we present are all inspired by experimental realizations of either synthetic, biomimetic or living systems. Based on minimal ingredients, they are meant to bring a simple and synthetic understanding of the complex phenomenology of active matter.Comment: Lecture notes for the international summer school "Fundamental Problems in Statistical Physics" 2017 in Brunec

Collective pairing of resonantly coupled microcavity polaritons

We consider the possible phases of microcavity polaritons tuned near a bipolariton Feshbach resonance. We show that, as well as the regular polariton superfluid phase, a "molecular" superfluid exists, with (quasi-)long-range order only for pairs of polaritons. We describe the experimental signatures of this state. Using variational approaches we find the phase diagram (critical temperature, density and exciton-photon detuning). Unlike ultracold atoms, the molecular superfluid is not inherently unstable, and our phase diagram suggests it is attainable in current experiments.Comment: paper (4 pages, 3 figures), Supplemental Material (7 pages, 8 figures

Chain graph models of multivariate regression type for categorical data

We discuss a class of chain graph models for categorical variables defined by what we call a multivariate regression chain graph Markov property. First, the set of local independencies of these models is shown to be Markov equivalent to those of a chain graph model recently defined in the literature. Next we provide a parametrization based on a sequence of generalized linear models with a multivariate logistic link function that captures all independence constraints in any chain graph model of this kind.Comment: Published in at http://dx.doi.org/10.3150/10-BEJ300 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

Hydrodynamics of Turning Flocks

We present a hydrodynamic model of flocking that generalizes the familiar Toner-Tu equations to incorporate turning inertia of well-polarized flocks. The continuum equations controlled by only two dimensionless parameters, orientational inertia and alignment strength, are derived by coarse graining the inertial spin model recently proposed by Cavagna et al. The interplay between orientational inertia and bend elasticity of the flock yields anisotropic spin waves that mediate the propagation of turning information throughout the flock. The coupling between spin current density to the local vorticity field through a nonlinear friction gives rise to a hydrodynamic mode with angular-dependent propagation speed at long wavelength. This mode goes unstable as a result of the growth of bend and splay deformations augmented by the spin wave, signaling the transition to complex spatio-temporal patterns of continuously turning and swirling flocks.Comment: 12 pages, 3 figure

Dipolar fermions in a multilayer geometry

We investigate the behavior of identical dipolar fermions with aligned dipole moments in two-dimensional multilayers at zero temperature. We consider density instabilities that are driven by the attractive part of the dipolar interaction and, for the case of bilayers, we elucidate the properties of the stripe phase recently predicted to exist in this interaction regime. When the number of layers is increased, we find that this "attractive" stripe phase exists for an increasingly larger range of dipole angles, and if the interlayer distance is sufficiently small, the stripe phase eventually spans the full range of angles, including the situation where the dipole moments are aligned perpendicular to the planes. In the limit of an infinite number of layers, we derive an analytic expression for the interlayer effects in the density-density response function and, using this result, we find that the stripe phase is replaced by a collapse of the dipolar system.Comment: 9 pages, 8 figure

Hydrodynamic and rheology of active polar filaments

The cytoskeleton provides eukaryotic cells with mechanical support and helps them perform their biological functions. It is a network of semiflexible polar protein filaments and many accessory proteins that bind to these filaments, regulate their assembly, link them to organelles and continuously remodel the network. Here we review recent theoretical work that aims to describe the cytoskeleton as a polar continuum driven out of equilibrium by internal chemical reactions. This work uses methods from soft condensed matter physics and has led to the formulation of a general framework for the description of the structure and rheology of active suspension of polar filaments and molecular motors.Comment: 30 pages, 5 figures. To appear in "Cell Motility", Peter Lenz, ed. (Springer, New York, 2007